Changes in version 0.99.2                        

Changes made in response to the Bioconductor package review (issue
#4227).

Single class system (S4)

  - Added the S4 class GrowthExperiment, which extends
    SummarizedExperiment with a validity method enforcing the canonical
    growth-assay layout. It is now the only data container in the
    package.
  - Removed the growkar_data S3 class and its constructor as_growkar(),
    along with the setOldClass()/setAs() pair used to coerce it. It
    duplicated the container constructor and was the source of the S3/S4
    tension noted in review.
  - Replaced as_summarized_experiment() with the S4 constructor
    GrowthExperiment() and standard coercion as(x, "GrowthExperiment").
    The constructor carries a metrics argument, preserving the only
    capability that was unique to as_growkar(). as(x,
    "SummarizedExperiment") is available in the other direction.
  - Converted the growkar_fit S3 class to the formal S4 class GrowthFit,
    with a validity method, show(), summary(), coef(), fitted(),
    residuals(), and nobs() methods, and the new accessors fit_sample(),
    fit_model(), fit_status(), fit_converged(), and fit_data().
  - extract_params() and augment_growth_fit() are now S4 generics with
    methods for GrowthFit.
  - The package now defines no S3 classes and registers no S3 methods.

Dependency separation

  - Moved ggplot2 and RColorBrewer from Imports to Suggests. The
    data-structure and analysis layers install and run without a
    graphics stack; the plot_*() functions check for the suggested
    packages at call time and raise an informative error when they are
    unavailable.

tidyomics interoperability

  - Added tidySummarizedExperiment to Suggests and documented tidy
    manipulation and display of growkar objects through the tidyomics
    stack rather than reimplementing those transformations.
  - Repositioned as_tidy_growth_data() explicitly as an import adapter
    for vendor plate-reader exports, which tidyomics does not cover.
  - Fixed a malformed code chunk in the introductory vignette.

                       Changes in version 0.99.0                        

  - Refactored the package around SummarizedExperiment as the canonical
    data model for microbial growth phenotyping workflows.
  - Added SE-native accessor and analysis helpers, including
    growth_assay(), timepoints(), sample_data(), growth_metrics(),
    phase_windows(), and fit_growth_models().
  - Standardized metadata conventions for derived summaries,
    exponential-phase windows, model fits, and analysis parameters
    stored in metadata(se).
  - Updated core analysis and plotting functions so tidy and wide inputs
    are standardized into the canonical SummarizedExperiment
    representation before downstream analysis.
  - Added plot_growth_curve_facets() for averaged, sample-family faceted
    growth curve visualization in multi-sample datasets.
  - Reworked the README, vignette, examples, and package metadata to
    present growkar as a Bioconductor-native package for high-throughput
    microbial growth phenotyping.